Metabolomic patterns in second-trimester amniotic fluid and maternal serum associated with fetal trisomy 21 Open Access

Abstract

Introduction. Trisomy 21, otherwise known as Down syndrome, is a genetic disorder characterized by the presence of three copies of chromosome 21 and is one of the most prevalent chromosomal disorders in the United States. Trisomy 21 is associated with several medical conditions and birth defects including cognitive impairment and congenital heart defects, yet the biological mechanisms driving the presentation of associated phenotypes remain largely unknown. Metabolomic analysis of a large set of paired second-trimester maternal serum and amniotic fluid samples was performed with the objective of (i) further elucidating the fetal metabolic fingerprint associated with trisomy 21 at mid-pregnancy and (ii) investigating whether metabolic pathways dysregulated in trisomy 21 fetuses offer potential mechanisms of disorder-associated phenotypes.

Methods. Untargeted, high-resolution metabolomic analysis using a dual liquid chromatography setup was performed on 39 pairs of maternal serum and amniotic fluid samples from trisomy 21 pregnancies and 81 control sample pairs. Discriminatory features were identified in both biofluids using partial least squares discriminant analysis and variable importance in projection scores after adjusting for covariates and used as input for metabolic pathway enrichment analysis using the program Mummichog.

Results. Variable selection and subsequent pathway analysis of the amniotic fluid features detected in this study produced a complex and extensive set of perturbations associated with trisomy 21. While results indicated dysregulation of multiple pathways related to lipid metabolism, nucleotide metabolism, and amino acid metabolism, vitamin B3 metabolism (p = 0.001) was shown to be the most significantly affected pathway in amniotic fluid. Glycine, serine, alanine, and threonine metabolism was significantly perturbed in both biological matrices of trisomy samples.

Conclusions. Results revealed a broad array of metabolic perturbations in second-trimester trisomy 21 amniotic fluid and offered novel insight into possible fetal origins of the cognitive impairment and age-related neurodegeneration frequently observed with the disorder. The untargeted analytical platform has laid a foundation for follow-up targeted studies to confirm metabolic associations of interest and their role in phenotypic outcome pathogenesis.

Table of Contents

List of Abbreviations ....... 1
1 Introduction ....... 3

1.1 Problem Statement ....... 3

1.2 Purpose Statement ....... 3
1.3 Significance Statement ....... 4
1.4 Definition of Terms ....... 4

2 Review of Literature ....... 5
3 Methodology ....... 9

3.1 Study Samples ....... 9
3.2 High-resolution LC-MS ....... 10

3.2.1 Feature Annotation ....... 11

3.3 Statistical Analysis ....... 12

3.3.1 Feature Selection ....... 13

3.4 Pathway Enrichment Analysis ....... 13

4 Results ....... 15

4.1 Global Metabolic Profiles in Serum and Amniotic Fluid ....... 15
4.2 Study Population ....... 16
4.3 Untargeted Metabolomic Analysis of Amniotic Fluid ....... 17

4.3.1 Feature Selection ....... 17
4.3.2 Pathway Analysis ....... 18

4.4 Untargeted Metabolomic Analysis of Maternal Serum ....... 19

4.4.1 Feature Selection ....... 19

4.4.2 Pathway Analysis ....... 20

5 Discussion ....... 21

5.1 Strengths and Limitations ....... 23

5.2 Future Directions ....... 24

References ....... 26

Appendix ....... 30

I Tables ....... 30
II Figures ....... 34

About this Master's Thesis

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School	Rollins School of Public Health
Department	Biostatistics and Bioinformatics
Degree	MSPH
Submission	Master's Thesis
Language	English
Research Field	Biology, Genetics Biology, Bioinformatics Environmental Health
Keyword	pregnancy metabolomics amniotic fluid Down syndrome
Committee Chair / Thesis Advisor	Yu, Tianwei, Emory University
Committee Members	Sherman, Stephanie, Emory University Fridovich-Keil, Judith, Emory University
Partnering Agencies	Emory University schools, faculty or affiliated programs National or regional non-profit organization (e.g., American Cancer Society)

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